# Mouse Colony Management

Labii Mouse Colony Management is built for research teams that need accurate, end-to-end control of mouse colony operations. The application centralizes mouseline setup, individual mouse records, mating plans, litter outcomes, and cage location tracking in one connected system. By keeping breeding, lineage, and housing data together, teams can reduce manual errors, improve colony visibility, and standardize colony workflows across staff and studies.

This application supports breeding management, genotyping-related tracking, and lifecycle monitoring from parental lines to offspring. Teams can view active colony statistics, automate generation calculations, create mice in bulk from litter records, and visualize lineage relationships for better breeding decisions and study planning.

Mouse Colony Management also integrates with Labii storage and custody capabilities for cage organization and handling traceability. Learn more on the [Mouse Colony Management landing page](https://www.labii.com/products/mouse-colony-management).

## Use Cases

### Academic and Translational Research Colonies

* Maintain standardized records for transgenic, knockout, and wild-type lines
* Track breeding performance by line to support experiment planning
* Monitor lineage and generation status for publication-ready documentation
* Coordinate mouse availability across multiple projects and lab members

### Preclinical and Regulated Workflows

* Maintain auditable records for breeding, litter, and animal movement events
* Support GLP-aligned documentation practices with complete activity history
* Improve traceability for protocol reviews and internal quality checks
* Keep cage assignment records synchronized with breeding and litter updates

### Core Facility or Shared Animal Resource Management

* Provide centralized colony oversight for multiple principal investigators
* Standardize intake and cataloging of new lines and breeders
* Reduce data duplication with one-click offspring creation from litter records
* Improve coordination between animal staff, scientists, and administrators

### Genotype-Aware Colony Planning

* Associate genotype data and colony metadata to each mouse record
* Visualize lineage to guide strategic pairings and avoid unwanted crosses
* Predict colony capacity based on active matings and litter progression
* Track downstream usage and movement through custody and storage records

## Application Data Model

Mouse Colony Management uses the following interconnected tables:

* **mc\_mouseline**: Defines each line, line-level settings, and aggregate colony statistics
* **mc\_mice**: Stores individual mouse identity, lifecycle status, lineage references, and metadata
* **mc\_mating**: Tracks breeding events, breeders, timing, and related cages and litters
* **mc\_litter**: Captures litter outcomes, parent linkage, litter size, generation, and offspring creation
* **core\_storage**: Tracks cage and physical storage location hierarchy
* **core\_chain\_of\_custody**: Records handling and movement events for traceability

{% hint style="info" %}
You can customize table fields, sections, and widgets to match your strain nomenclature, genotyping schema, and institutional workflow requirements.
{% endhint %}

## Getting Started

{% stepper %}
{% step %}
Open **Mouse Colony Management** from your applications menu in Labii.
{% endstep %}

{% step %}
Configure foundational settings:

* Define mouseline naming standards and line categories
* Set default lifecycle milestones (for example, wean and mature ages)
* Confirm status options for mice, mating, and litter records
  {% endstep %}

{% step %}
Set up cage and location infrastructure in **core\_storage** so mice, mating pairs, and litters can be assigned to physical housing locations.
{% endstep %}

{% step %}
Review user permissions to ensure only authorized members can create, update, or approve sensitive colony records.
{% endstep %}

{% step %}
Create your first mouseline and begin registering breeders and active colony mice.
{% endstep %}
{% endstepper %}

## Core Workflows

### 1) Configure Mouselines and Colony Baselines

Use this workflow to establish each mouse line and define operational baselines before active breeding.

{% stepper %}
{% step %}
Navigate to **mc\_mouseline** and select **Add New Record**.
{% endstep %}

{% step %}
Enter core line information:

* Line name and category
* Primary genotype descriptors
* Status (active, archived, or planned)
* Wean and mature age settings
  {% endstep %}

{% step %}
Save the record and verify line-level statistics panels for active mice, active matings, and active litters.
{% endstep %}
{% endstepper %}

### 2) Register Individual Mice and Track Lineage

Use this workflow to create high-quality, traceable records for each animal.

{% stepper %}
{% step %}
Navigate to **mc\_mice** and create a new mouse record.
{% endstep %}

{% step %}
Capture identification and biological details:

* Mouse identifier and sex
* Birth date or estimated age
* Current status and line assignment
* Genotype and related metadata
  {% endstep %}

{% step %}
Link parent or lineage relationships where available to support pedigree visualization.
{% endstep %}

{% step %}
Assign cage location using linked storage data so housing remains synchronized with animal records.
{% endstep %}
{% endstepper %}

### 3) Manage Breeding and Mating Records

Use this workflow to track pairings and maintain breeding traceability.

{% stepper %}
{% step %}
Open **mc\_mating** and create a new mating event.
{% endstep %}

{% step %}
Select breeder mice (single or multiple breeders, based on your workflow configuration).
{% endstep %}

{% step %}
Record mating details:

* Start date
* Cage assignment
* Mating status and notes
* Related mouseline context
  {% endstep %}

{% step %}
Save the record and monitor linked litter outcomes as they are added.
{% endstep %}
{% endstepper %}

### 4) Record Litters and Create Offspring in Bulk

Use this workflow to convert breeding outcomes into structured animal records quickly.

{% stepper %}
{% step %}
Navigate to **mc\_litter** and create a litter record linked to its mating event.
{% endstep %}

{% step %}
Enter litter details:

* Parent references
* Birth date
* Litter size
* Cage assignment
* Notes on health or observations
  {% endstep %}

{% step %}
Review the automatically calculated generation value.
{% endstep %}

{% step %}
Click **Create Mice** to automatically generate individual offspring records based on litter size.
{% endstep %}

{% step %}
Update each offspring record with sex, genotype results, and lifecycle status as data becomes available.
{% endstep %}
{% endstepper %}

### 5) Track Cage Location and Custody Events

Use this workflow to preserve housing and movement traceability for compliance and operational clarity.

{% stepper %}
{% step %}
Use **core\_storage** to define cage hierarchy (facility, room, rack, cage).
{% endstep %}

{% step %}
Assign storage locations to mice, mating pairs, and litters.
{% endstep %}

{% step %}
Record cage transfers, handling handoffs, or movement events in **core\_chain\_of\_custody**.
{% endstep %}

{% step %}
Review movement history during audits, protocol checks, and incident investigations.
{% endstep %}
{% endstepper %}

## Advanced Features

### Process Integration for Colony Lifecycle Automation

Labii process integration can orchestrate common colony events, including mating initiation, litter updates, weaning transitions, and status changes.

{% hint style="success" %}
Use workflow steps and automation rules to reduce repetitive data entry and enforce consistent colony procedures across teams.
{% endhint %}

### Automatic Generation Calculation

Generation is calculated automatically in litter workflows to minimize manual errors and keep lineage records consistent.

### Lineage Visualization

Lineage tools provide pedigree-like context for each mouse, helping teams make informed breeding and genotyping decisions.

### Flexible Data Customization

All major forms can be adapted to capture study-specific metadata such as genotype call method, phenotype tags, and protocol identifiers.

## Troubleshooting

### Issue: Offspring records are not created from a litter

**Symptoms**: The **Create Mice** action does not generate expected mouse records.

{% stepper %}
{% step %}
Verify that litter size is entered as a valid numeric value in the litter record.
{% endstep %}

{% step %}
Confirm the litter is saved and linked to a valid mating record.
{% endstep %}

{% step %}
Check user permissions for creating records in **mc\_mice**.
{% endstep %}

{% step %}
Retry **Create Mice** and confirm record creation in the mice list view.
{% endstep %}
{% endstepper %}

### Issue: Cage location appears inconsistent across records

**Symptoms**: Mouse, mating, or litter records show different housing locations than expected.

{% stepper %}
{% step %}
Verify that storage hierarchy values in **core\_storage** are active and not archived.
{% endstep %}

{% step %}
Review recent movement entries in **core\_chain\_of\_custody** for updates or transfers.
{% endstep %}

{% step %}
Standardize location update rules so all related records are updated at transfer time.
{% endstep %}
{% endstepper %}

### Issue: Lineage view is incomplete

**Symptoms**: Parent or offspring relationships are missing in lineage visualization.

{% stepper %}
{% step %}
Check that parent references are populated correctly in mouse and litter records.
{% endstep %}

{% step %}
Confirm records are linked to the same organization and available in active scope.
{% endstep %}

{% step %}
Reload the record detail page after saving relationship updates.
{% endstep %}
{% endstepper %}